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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 0.9

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        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2017-04-05, 10:04 based on data in: /data/curtis/Sequence/all_run


        General Statistics

        Showing 192/192 rows and 5/7 columns.
        Sample Name% AssignedM Assigned% Dups% GCM Seqs
        P6975_101_S1_L001_R1_001
        61.6%
        6.1
        49.8%
        47%
        8.2
        P6975_101_S1_L002_R1_001
        61.6%
        6.2
        49.7%
        47%
        8.4
        P6975_102_S2_L001_R1_001
        62.8%
        8.3
        51.2%
        48%
        11.0
        P6975_102_S2_L002_R1_001
        62.8%
        8.4
        51.0%
        48%
        11.2
        P6975_103_S3_L001_R1_001
        62.6%
        6.8
        50.6%
        48%
        8.9
        P6975_103_S3_L002_R1_001
        62.5%
        6.9
        50.9%
        48%
        9.1
        P6975_104_S4_L001_R1_001
        62.8%
        6.7
        49.3%
        48%
        8.9
        P6975_104_S4_L002_R1_001
        62.7%
        6.9
        49.8%
        48%
        9.1
        P6975_105_S25_L003_R1_001
        63.5%
        6.6
        49.9%
        48%
        8.7
        P6975_105_S25_L004_R1_001
        63.6%
        6.6
        49.5%
        48%
        8.7
        P6975_106_S26_L003_R1_001
        63.8%
        7.1
        52.3%
        48%
        9.3
        P6975_106_S26_L004_R1_001
        63.8%
        7.1
        51.8%
        48%
        9.3
        P6975_107_S27_L003_R1_001
        63.6%
        7.3
        50.5%
        48%
        9.6
        P6975_107_S27_L004_R1_001
        63.7%
        7.3
        50.0%
        48%
        9.6
        P6975_108_S28_L003_R1_001
        63.0%
        6.8
        49.7%
        47%
        9.0
        P6975_108_S28_L004_R1_001
        63.0%
        6.8
        49.2%
        47%
        9.0
        P6975_109_S5_L001_R1_001
        62.5%
        6.7
        50.3%
        49%
        8.8
        P6975_109_S5_L002_R1_001
        62.5%
        6.8
        50.5%
        49%
        9.0
        P6975_110_S6_L001_R1_001
        61.2%
        7.8
        53.2%
        50%
        10.3
        P6975_110_S6_L002_R1_001
        61.2%
        7.9
        53.5%
        50%
        10.6
        P6975_111_S7_L001_R1_001
        63.5%
        6.7
        50.1%
        49%
        8.7
        P6975_111_S7_L002_R1_001
        63.5%
        6.8
        50.2%
        49%
        8.9
        P6975_112_S8_L001_R1_001
        65.0%
        7.7
        49.6%
        49%
        9.9
        P6975_112_S8_L002_R1_001
        64.9%
        7.8
        49.5%
        49%
        10.0
        P6975_113_S29_L003_R1_001
        63.4%
        7.0
        49.1%
        48%
        9.1
        P6975_113_S29_L004_R1_001
        63.4%
        7.0
        48.7%
        48%
        9.2
        P6975_114_S30_L003_R1_001
        62.9%
        7.0
        49.6%
        48%
        9.3
        P6975_114_S30_L004_R1_001
        62.9%
        7.0
        49.3%
        48%
        9.3
        P6975_115_S31_L003_R1_001
        62.2%
        7.6
        51.6%
        48%
        10.2
        P6975_115_S31_L004_R1_001
        62.2%
        7.7
        51.5%
        48%
        10.3
        P6975_116_S32_L003_R1_001
        62.5%
        6.9
        48.7%
        48%
        9.2
        P6975_116_S32_L004_R1_001
        62.6%
        6.9
        48.2%
        48%
        9.2
        P6975_117_S9_L001_R1_001
        64.5%
        3.9
        41.0%
        49%
        5.0
        P6975_117_S9_L002_R1_001
        64.5%
        3.8
        41.3%
        49%
        5.0
        P6975_118_S10_L001_R1_001
        63.5%
        4.9
        45.0%
        49%
        6.5
        P6975_118_S10_L002_R1_001
        63.5%
        4.9
        45.1%
        49%
        6.5
        P6975_119_S11_L001_R1_001
        64.7%
        4.2
        43.8%
        50%
        5.4
        P6975_119_S11_L002_R1_001
        64.7%
        4.1
        43.7%
        50%
        5.3
        P6975_120_S12_L001_R1_001
        63.3%
        3.8
        42.7%
        50%
        5.0
        P6975_120_S12_L002_R1_001
        63.3%
        3.8
        42.8%
        50%
        5.0
        P6975_121_S33_L003_R1_001
        63.1%
        4.6
        45.5%
        48%
        6.1
        P6975_121_S33_L004_R1_001
        63.1%
        4.7
        44.5%
        48%
        6.2
        P6975_122_S34_L003_R1_001
        62.0%
        4.9
        45.7%
        48%
        6.6
        P6975_122_S34_L004_R1_001
        62.0%
        5.0
        44.6%
        48%
        6.6
        P6975_123_S35_L003_R1_001
        61.4%
        4.7
        45.8%
        48%
        6.3
        P6975_123_S35_L004_R1_001
        61.4%
        4.8
        44.4%
        48%
        6.3
        P6975_124_S36_L003_R1_001
        61.0%
        4.2
        43.9%
        48%
        5.7
        P6975_124_S36_L004_R1_001
        61.0%
        4.3
        42.2%
        48%
        5.7
        P6975_125_S13_L001_R1_001
        63.2%
        7.8
        51.6%
        49%
        10.1
        P6975_125_S13_L002_R1_001
        63.2%
        7.9
        51.7%
        49%
        10.3
        P6975_126_S14_L001_R1_001
        63.7%
        9.2
        52.8%
        49%
        11.9
        P6975_126_S14_L002_R1_001
        63.7%
        9.3
        53.0%
        49%
        12.1
        P6975_127_S15_L001_R1_001
        62.4%
        7.8
        49.9%
        49%
        10.4
        P6975_127_S15_L002_R1_001
        62.4%
        7.9
        50.2%
        49%
        10.5
        P6975_128_S16_L001_R1_001
        62.1%
        7.7
        53.5%
        49%
        10.2
        P6975_128_S16_L002_R1_001
        62.0%
        7.9
        53.7%
        49%
        10.4
        P6975_129_S37_L003_R1_001
        62.7%
        8.3
        53.1%
        48%
        11.0
        P6975_129_S37_L004_R1_001
        62.7%
        8.4
        52.9%
        48%
        11.0
        P6975_130_S38_L003_R1_001
        62.1%
        8.0
        52.0%
        48%
        10.6
        P6975_130_S38_L004_R1_001
        62.1%
        8.0
        51.7%
        48%
        10.7
        P6975_131_S39_L003_R1_001
        63.2%
        7.4
        50.8%
        48%
        9.7
        P6975_131_S39_L004_R1_001
        63.2%
        7.5
        50.5%
        48%
        9.8
        P6975_132_S40_L003_R1_001
        61.7%
        8.5
        51.2%
        47%
        11.6
        P6975_132_S40_L004_R1_001
        61.7%
        8.6
        51.2%
        47%
        11.7
        P6975_133_S17_L001_R1_001
        63.2%
        7.6
        51.3%
        49%
        9.9
        P6975_133_S17_L002_R1_001
        63.2%
        7.8
        51.5%
        49%
        10.1
        P6975_134_S18_L001_R1_001
        63.2%
        9.0
        53.7%
        48%
        11.7
        P6975_134_S18_L002_R1_001
        63.1%
        9.1
        54.0%
        48%
        11.9
        P6975_135_S19_L001_R1_001
        63.9%
        8.4
        53.8%
        49%
        11.0
        P6975_135_S19_L002_R1_001
        63.8%
        8.6
        54.1%
        49%
        11.2
        P6975_136_S20_L001_R1_001
        62.6%
        8.6
        53.7%
        49%
        11.2
        P6975_136_S20_L002_R1_001
        62.6%
        8.7
        53.9%
        49%
        11.4
        P6975_137_S41_L003_R1_001
        62.6%
        7.8
        50.7%
        48%
        10.4
        P6975_137_S41_L004_R1_001
        62.7%
        7.8
        50.9%
        48%
        10.4
        P6975_138_S42_L003_R1_001
        61.9%
        8.3
        51.0%
        47%
        11.1
        P6975_138_S42_L004_R1_001
        61.9%
        8.3
        50.7%
        47%
        11.2
        P6975_139_S43_L003_R1_001
        61.4%
        8.0
        51.2%
        48%
        10.7
        P6975_139_S43_L004_R1_001
        61.4%
        8.0
        50.9%
        48%
        10.8
        P6975_140_S44_L003_R1_001
        62.6%
        8.4
        51.5%
        47%
        11.1
        P6975_140_S44_L004_R1_001
        62.6%
        8.4
        51.2%
        47%
        11.1
        P6975_141_S21_L001_R1_001
        63.0%
        7.9
        51.3%
        49%
        10.3
        P6975_141_S21_L002_R1_001
        63.0%
        8.1
        51.5%
        49%
        10.5
        P6975_142_S22_L001_R1_001
        61.8%
        10.2
        54.9%
        49%
        13.6
        P6975_142_S22_L002_R1_001
        61.8%
        10.4
        54.8%
        49%
        13.9
        P6975_143_S23_L001_R1_001
        63.9%
        8.5
        52.4%
        49%
        11.0
        P6975_143_S23_L002_R1_001
        63.9%
        8.6
        52.6%
        49%
        11.2
        P6975_144_S24_L001_R1_001
        63.6%
        8.5
        52.9%
        50%
        11.0
        P6975_144_S24_L002_R1_001
        63.6%
        8.7
        53.4%
        50%
        11.2
        P6975_145_S45_L003_R1_001
        62.2%
        8.4
        51.7%
        48%
        11.1
        P6975_145_S45_L004_R1_001
        62.2%
        8.4
        51.4%
        48%
        11.2
        P6975_146_S46_L003_R1_001
        61.7%
        8.4
        52.0%
        48%
        11.2
        P6975_146_S46_L004_R1_001
        61.8%
        8.4
        51.7%
        48%
        11.2
        P6975_147_S47_L003_R1_001
        62.5%
        8.7
        51.9%
        48%
        11.6
        P6975_147_S47_L004_R1_001
        62.6%
        8.7
        51.7%
        48%
        11.6
        P6975_148_S48_L003_R1_001
        61.2%
        8.2
        53.4%
        48%
        11.0
        P6975_148_S48_L004_R1_001
        61.1%
        8.2
        53.0%
        48%
        11.0
        P6975_149_S49_L005_R1_001
        62.5%
        7.2
        52.6%
        49%
        9.4
        P6975_149_S49_L006_R1_001
        62.4%
        7.1
        52.1%
        49%
        9.3
        P6975_150_S50_L005_R1_001
        63.7%
        8.3
        50.1%
        50%
        10.7
        P6975_150_S50_L006_R1_001
        63.7%
        8.2
        49.7%
        50%
        10.7
        P6975_151_S51_L005_R1_001
        63.7%
        8.5
        51.3%
        50%
        11.0
        P6975_151_S51_L006_R1_001
        63.7%
        8.4
        50.9%
        50%
        11.0
        P6975_152_S52_L005_R1_001
        62.0%
        8.2
        55.7%
        50%
        11.0
        P6975_152_S52_L006_R1_001
        62.0%
        8.2
        55.1%
        50%
        10.9
        P6975_153_S73_L007_R1_001
        61.1%
        7.4
        51.8%
        48%
        9.9
        P6975_153_S73_L008_R1_001
        61.1%
        7.3
        44.2%
        48%
        9.9
        P6975_154_S74_L007_R1_001
        61.3%
        7.6
        52.0%
        48%
        10.1
        P6975_154_S74_L008_R1_001
        61.3%
        7.5
        44.1%
        48%
        10.1
        P6975_155_S75_L007_R1_001
        57.8%
        7.4
        54.1%
        48%
        10.2
        P6975_155_S75_L008_R1_001
        57.8%
        7.3
        46.5%
        48%
        10.2
        P6975_156_S76_L007_R1_001
        60.4%
        7.6
        51.1%
        47%
        10.4
        P6975_156_S76_L008_R1_001
        60.4%
        7.6
        43.4%
        47%
        10.4
        P6975_157_S53_L005_R1_001
        60.7%
        7.6
        53.0%
        48%
        10.2
        P6975_157_S53_L006_R1_001
        60.7%
        7.5
        52.6%
        48%
        10.2
        P6975_158_S54_L005_R1_001
        61.3%
        8.4
        52.1%
        49%
        11.1
        P6975_158_S54_L006_R1_001
        61.3%
        8.3
        51.7%
        49%
        11.1
        P6975_159_S55_L005_R1_001
        58.2%
        8.0
        58.5%
        48%
        11.0
        P6975_159_S55_L006_R1_001
        58.2%
        8.0
        57.9%
        48%
        10.9
        P6975_160_S56_L005_R1_001
        61.6%
        7.7
        53.3%
        50%
        10.1
        P6975_160_S56_L006_R1_001
        61.6%
        7.7
        52.7%
        50%
        10.1
        P6975_161_S77_L007_R1_001
        57.8%
        7.3
        53.0%
        48%
        10.4
        P6975_161_S77_L008_R1_001
        57.9%
        7.3
        45.4%
        48%
        10.4
        P6975_162_S78_L007_R1_001
        62.2%
        8.0
        51.3%
        48%
        10.7
        P6975_162_S78_L008_R1_001
        62.2%
        8.0
        43.3%
        48%
        10.6
        P6975_163_S79_L007_R1_001
        62.6%
        7.8
        51.8%
        48%
        10.2
        P6975_163_S79_L008_R1_001
        62.6%
        7.7
        44.1%
        48%
        10.2
        P6975_164_S80_L007_R1_001
        61.3%
        8.7
        53.1%
        48%
        11.8
        P6975_164_S80_L008_R1_001
        61.4%
        8.6
        44.5%
        48%
        11.7
        P6975_165_S57_L005_R1_001
        62.0%
        7.4
        51.9%
        48%
        9.9
        P6975_165_S57_L006_R1_001
        61.9%
        7.4
        51.7%
        48%
        9.9
        P6975_166_S58_L005_R1_001
        64.2%
        8.5
        52.0%
        49%
        11.1
        P6975_166_S58_L006_R1_001
        64.2%
        8.5
        51.4%
        48%
        11.0
        P6975_167_S59_L005_R1_001
        62.5%
        8.2
        53.6%
        50%
        10.7
        P6975_167_S59_L006_R1_001
        62.5%
        8.1
        53.1%
        50%
        10.6
        P6975_168_S60_L005_R1_001
        62.2%
        8.4
        54.5%
        50%
        11.0
        P6975_168_S60_L006_R1_001
        62.2%
        8.3
        54.2%
        50%
        11.0
        P6975_169_S81_L007_R1_001
        60.0%
        8.2
        54.6%
        48%
        11.0
        P6975_169_S81_L008_R1_001
        60.0%
        8.2
        46.0%
        48%
        11.0
        P6975_170_S82_L007_R1_001
        61.6%
        8.2
        53.5%
        47%
        10.9
        P6975_170_S82_L008_R1_001
        61.6%
        8.2
        44.9%
        47%
        10.9
        P6975_171_S83_L007_R1_001
        56.9%
        7.4
        51.5%
        48%
        10.5
        P6975_171_S83_L008_R1_001
        56.9%
        7.4
        44.0%
        48%
        10.5
        P6975_172_S84_L007_R1_001
        60.6%
        7.9
        51.8%
        48%
        10.6
        P6975_172_S84_L008_R1_001
        60.6%
        7.8
        44.4%
        48%
        10.6
        P6975_173_S61_L005_R1_001
        63.4%
        8.5
        53.6%
        48%
        11.0
        P6975_173_S61_L006_R1_001
        63.3%
        8.4
        53.2%
        48%
        11.0
        P6975_174_S62_L005_R1_001
        64.3%
        8.5
        52.1%
        50%
        10.9
        P6975_174_S62_L006_R1_001
        64.2%
        8.4
        51.9%
        50%
        10.8
        P6975_175_S63_L005_R1_001
        63.1%
        8.5
        53.9%
        50%
        11.1
        P6975_175_S63_L006_R1_001
        63.1%
        8.5
        53.6%
        50%
        11.1
        P6975_176_S64_L005_R1_001
        62.2%
        8.1
        53.7%
        50%
        10.8
        P6975_176_S64_L006_R1_001
        62.2%
        8.1
        53.0%
        50%
        10.8
        P6975_177_S85_L007_R1_001
        61.9%
        8.4
        52.5%
        48%
        11.4
        P6975_177_S85_L008_R1_001
        61.8%
        8.4
        44.1%
        48%
        11.4
        P6975_178_S86_L007_R1_001
        62.1%
        7.8
        50.5%
        47%
        10.6
        P6975_178_S86_L008_R1_001
        62.1%
        7.8
        42.9%
        47%
        10.6
        P6975_179_S87_L007_R1_001
        61.9%
        8.8
        52.2%
        48%
        11.9
        P6975_179_S87_L008_R1_001
        61.9%
        8.8
        43.4%
        48%
        11.9
        P6975_180_S88_L007_R1_001
        61.6%
        8.1
        52.6%
        48%
        10.8
        P6975_180_S88_L008_R1_001
        61.6%
        8.0
        44.3%
        48%
        10.7
        P6975_181_S65_L005_R1_001
        61.7%
        8.4
        55.8%
        50%
        11.0
        P6975_181_S65_L006_R1_001
        61.7%
        8.4
        55.4%
        50%
        11.0
        P6975_182_S66_L005_R1_001
        63.8%
        9.2
        51.1%
        49%
        12.0
        P6975_182_S66_L006_R1_001
        63.8%
        9.2
        50.8%
        49%
        11.9
        P6975_183_S67_L005_R1_001
        62.6%
        8.4
        51.2%
        48%
        11.1
        P6975_183_S67_L006_R1_001
        62.6%
        8.3
        51.2%
        48%
        11.1
        P6975_184_S68_L005_R1_001
        62.1%
        8.0
        54.3%
        49%
        10.4
        P6975_184_S68_L006_R1_001
        62.0%
        7.9
        53.6%
        49%
        10.3
        P6975_185_S89_L007_R1_001
        61.7%
        7.8
        51.6%
        48%
        10.4
        P6975_185_S89_L008_R1_001
        61.6%
        7.8
        43.7%
        48%
        10.3
        P6975_186_S90_L007_R1_001
        62.6%
        7.9
        51.7%
        47%
        10.6
        P6975_186_S90_L008_R1_001
        62.6%
        7.9
        43.7%
        47%
        10.5
        P6975_187_S91_L007_R1_001
        62.0%
        7.8
        50.6%
        48%
        10.4
        P6975_187_S91_L008_R1_001
        62.1%
        7.7
        42.9%
        48%
        10.3
        P6975_188_S92_L007_R1_001
        62.4%
        7.9
        52.8%
        48%
        10.4
        P6975_188_S92_L008_R1_001
        62.4%
        7.9
        44.9%
        48%
        10.4
        P6975_189_S69_L005_R1_001
        62.6%
        8.7
        52.1%
        48%
        11.5
        P6975_189_S69_L006_R1_001
        62.6%
        8.6
        51.9%
        48%
        11.4
        P6975_190_S70_L005_R1_001
        62.9%
        9.5
        53.4%
        48%
        12.5
        P6975_190_S70_L006_R1_001
        62.9%
        9.5
        53.0%
        48%
        12.4
        P6975_191_S71_L005_R1_001
        63.0%
        9.3
        53.6%
        49%
        12.1
        P6975_191_S71_L006_R1_001
        63.0%
        9.2
        53.2%
        49%
        12.0
        P6975_192_S72_L005_R1_001
        55.6%
        7.9
        54.5%
        49%
        11.4
        P6975_192_S72_L006_R1_001
        55.6%
        7.9
        54.3%
        49%
        11.4
        P6975_193_S93_L007_R1_001
        48.4%
        6.4
        59.6%
        48%
        11.0
        P6975_193_S93_L008_R1_001
        48.3%
        6.4
        52.7%
        48%
        11.0
        P6975_194_S94_L007_R1_001
        49.7%
        5.4
        58.0%
        48%
        8.9
        P6975_194_S94_L008_R1_001
        49.7%
        5.4
        52.0%
        48%
        8.8
        P6975_195_S95_L007_R1_001
        49.7%
        5.9
        63.5%
        48%
        9.6
        P6975_195_S95_L008_R1_001
        49.7%
        5.9
        55.8%
        48%
        9.6
        P6975_196_S96_L007_R1_001
        59.3%
        10.9
        55.0%
        47%
        15.2
        P6975_196_S96_L008_R1_001
        59.2%
        10.9
        42.8%
        47%
        15.2

        HTSeq Count

        HTSeq Count is part of the HTSeq Python package - it takes a file with aligned sequencing reads, plus a list of genomic features and counts how many reads map to each feature.

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        Samtools

        Samtools is a suite of programs for interacting with high-throughput sequencing data.

        Samtools Flagstat

        This module parses the output from samtools flagstat. All numbers in millions.

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        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Quality Histograms

        The mean quality value across each base position in the read. See the FastQC help.

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        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality. See the FastQC help.

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        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called. See the FastQC help.

        Click a heatmap row to see a line plot for that dataset.

        rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content. See the FastQC help.

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        Per Base N Content

        The percentage of base calls at each position for which an N was called. See the FastQC help.

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        Sequence Length Distribution

        All samples have sequences of a single length (51bp).


        Sequence Duplication Levels

        The relative level of duplication found for every sequence. See the FastQC help.

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        Overrepresented sequences

        The total amount of overrepresented sequences found in each library. See the FastQC help for further information.

        192 samples had less than 1% of reads made up of overrepresented sequences

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. See the FastQC help. Only samples with ≥ 0.1% adapter contamination are shown.

        No samples found with any adapter contamination > 0.1%